Curator Dashboard

Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

A web catalog of over 1M antibodies from hundreds of different companies and other research supplies. Biocompare has made large quantities of data available to the antibodyregistry.org facilitating tagging important research reagents to literature and continues to work with the antibodyregistry.

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• SciCrunch
• 17 years ago - by Anonymous

A tool for visualizing displacement fields estimated in association with image registration. Based on the displacement vector field, a mesh is generated for visualization. The mesh can be color mapped with the jacobian determinant at each point for better localization of regions that undergo compression or expansion. Other key features include: view synchronization, adjustable mesh resolution, and conversion from deformation and HAMMER displacement fields.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Flow cytometry facility provides instrumentation for data acquisition, analysis, and cell sorting, technical expertise to interpret results and develop methods. Offers information about new techniques, and applications of flow cytometry through workshops and seminars, and provides training to interested facility users. Individual consultation services are available.Human Immune Monitoring Facility provides immune profiling, sample preparation,clinical trial support, technical expertise to clinical investigators and research scientists.Services include multispectral flow cytometry, metabolic analysis, blood services such as PBMC isolation and serum/plasma extraction, and full spectrum of immunological services.Offers custom assays and biobanking services upon request.Offers training, assisted, unassisted, and technician operated modalities for all instruments and will meet investigators at their desired level of engagement.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

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• SciCrunch
• 14 years ago - by Anonymous

A user-friendly graphical-user-interface (GUI)-based toolbox (MATLAB) for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, and interactive exploration of results.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.

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• SciCrunch
• 13 years ago - by Anonymous

Ontology (http://www.bioassayontology.org/bao_gpcr) that describes pharmacology, biochemistry and physiology of these important and therapeutically promising class of academic and pharmaceutical research targets. Incorporation and comparison of various small molecule screening data sets, such as those deposited in PubChem, ChEMBL, KEGG, PDSP, and/or IUPHAR databases, requires a formalized electronic organization system. In order to bridge the gap between the overflow of HTS data and the bottleneck of integrated analysis tools, herein, we provide the first comprehensive GPCR ontology. The development and utility of GPCR ontology was based on previously developed BioAssay Ontology (BAO). The GPCR ontology contains information about biochemical, pharmacological, and functional properties of individual GPCRs as well as GPCR-selective ligands inclusive of their HTS screening results and other records. This provides the first all-inclusive GPCR ontology with all available data to model the relationship between the GPCR binding sites and their physiologic and pharmacologic role in physiology via small molecule chemical structures. We developed this system using emerging semantic technologies, by leveraging existing and descriptive domain level ontologies.

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• SciCrunch
• 13 years ago - by Anonymous

A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool for efficiently solving large scale sequence matching tasks.

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• RRID-Legacy
• 6 years ago - submitted by John Hamilton

Software providing a scoring technique for stability selection, which improves the performance of feature selection with LARS. TIGRESS can be run online through the GenePattern platform (GP-DREAM, http://dream.broadinstitute.org).

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• SciCrunch
• 13 years ago - by Anonymous

A segmentation tool for the segmentation of a lung from CT images. The sofware can be run in two modes: fully automatic and semi-automatic with manual seeding by the user. The software also allows the user to perform basic filtering operations and manual correction to the segmentation. The VTK-based rendering implementation, along with option to view in axial, coronal, and sagittal, provides the user with better visualization of the segmented lung.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Analysis of elemental composition of biological tissues and fluids by Inductively Coupled Plasma Mass spectrometry. Analysis of Arsenic species in urine and blood by chromatography-ICP-MS. Laser ablation analysis of tissue sections for imaging of elemental distributions.

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• SciCrunch
• 13 years ago - by Anonymous

Francisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. rancisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. Please visit the following sections of the website for more details about the tools currently available and those to be available in the near future. News 04/17/2008 F. novicida transposon mutant orders are now being handled by BEI Resources. 03/25/2008 New features have been added to the PSAT synteny analysis tool including a printer friendly version of the genomic neighborhood graphic, a text output of homologs in a region in spreadsheet format, and an option for displaying multiple alignments for a gene against a single comparison genome. 02/07/2008 Proteomics experimental data for F. novicida are now integrated into our genome browser. 02/05/2008 Updated genome annotations can now be submitted using the Panda tool. Your participation is encouraged. Please see the Panda page for more information. 02/04/2008 F. holarctica FTA is now available from Genbank (NC_009749) and has been added to our genome browser Tools Name Description Get surrounding sequence Given a gene, other genome feature, or genome coordinate, displays in FASTA format the surrounding sequence a specified number of nucleotides upstream and downstream Synteny Tool Analyze potential regions of local synteny between the Francisella genomes and any other published bacterial genome

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• SciCrunch
• 17 years ago - by Anonymous

Structure from motion algorithms repository. Common interface for various sfm algorithms.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Provides access to conventional transmission electron microscope and associated sample processing services.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.

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• SciCrunch
• 12 years ago - by Anonymous

A full featured and extensible application which simulates biological neural networks using graphic tools which edit neurons and networks, run the simulation and analyze results. It is written in C and runs on Unix and Windows. It is specifically targeted for neuroscientists who are less experienced with computer programming.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Open source software R package for modeling and correcting Illumina sequenced amplicon errors. Fast and accurate sample inference from amplicon data with single nucleotide resolution.

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• RRID
• 3 years ago - by Anonymous

The Brain Trauma Foundation (BTF) is a national non-profit organization dedicated to improving the outcome of traumatic brain injury (TBI) patients worldwide by developing best practices guidelines, quality improvement programs, conducting clinical research, and educating medical professionals and consumers. Our efforts also focus on public education aimed at increasing awareness and understanding of the symptoms of a concussion. Our goal is to better educate coaches, nurses, athletes, parents and all citizens about the importance of recognizing concussions and taking the appropriate steps to ensure people receive appropriate care. Also by educating healthcare professionals on the immediate care for coma patients, we estimate that thousands of lives could be saved each year in the U.S., millions worldwide, and more would be spared life-long disabilities. Research has proven that all brain damage does not occur at the moment of impact but rather evolves over the ensuing hours and days after the initial injury, due to brain swelling and inadequate oxygen and blood flow to the injured brain. In most cases, this secondary damage can be controlled by applying scientific, evidence-based diagnostic and treatment Guidelines, which BTF has developed with medical organizations and physicians with expertise in TBI. BTF offers updated continuing education activities for all levels of health care professionals caring for TBI patients. The online activities include recorded presentations, live web-based lectures, and interactive learning modules based on the latest scientific-evidence. Also available on the BTF Learning Portal is an online version of the EMS course developed in coordination with National Highway Traffic Safety Administration. The Brain Trauma Foundation leads the way in cutting-edge clinical research on Traumatic Brain Injury (TBI). Improving diagnosis and treatment of TBI requires a focus on clinical research. Our mission is to improve the outcome of TBI patients worldwide. BTF's research spans the spectrum from concussion to coma. BTF is conducting innovative research into the cause diagnosis of concussion. Also, BTF develops Best TBI Practice Guidelines, which when followed can significantly improve a patient's outcome. The Foundation is currently conducting studies and leading consortiums of investigators from multiple universities and disciplines in many TBI research areas that will have immediate impact on patient outcomes.

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• SciCrunch
• 16 years ago - by Anonymous